Rep. Darrell Issa seems to have retained his seat in San Diego's 49th District, following a close contest with retired Marine Col. Doug Applegate.

UPDATE: 5 a.m., Nov. 9, 2016:

Rep. Darrell Issa, R-Vista, held off a challenge from former Marine Col. Doug Applegate, a Democrat, in his re-election bid.

First elected to Congress 16 years ago, Issa won a bare majority of votes in the June primary election after years of being re-elected by double-digit margins.

In the months since, Democrats poured a considerable amount of money into the race, and narrowed a deficit in voter registration in the San Diego County portion of the district. Issa also represents part of southern Orange County.

President Barack Obama commented on the race last month during a fundraiser for Democratic presidential nominee Hillary Clinton in La Jolla, calling an Issa mailer "the definition of chutzpah."

As the head of a House oversight committee, Issa led numerous investigations into Obama's and Clinton's role in the deaths of four Americans — including three with ties to San Diego — in Benghazi, Libya, in 2012.

His latest re-election try turned into a political slugfest, forcing Issa to spend more time campaigning in his district than in previous elections. The result was notably close, with just a few thousand votes separating the combatants.

Applegate and other Democrats hammered Issa during the campaign for endorsing businessman Donald Trump for president, after spending most of the primary season backing Florida Sen. Marco Rubio.

"If you start compromising what you believe and who you're going to support based on your political well-being, you're going to stand for nothing," Issa told Fox5 San Diego. Trump's statements were "reprehensible" but Democrat Hillary Clinton disqualified herself by mishandling classified material while she was secretary of state, he said.

Other members of the region's five-representative House delegation won in comfortable fashion. They include Republican Duncan D. Hunter, and Democrats Susan Davis, Scott Peters and Juan Vargas.

UPDATE: 11:40 p.m., Nov. 8, 2016:

Rep. Darrell Issa is maintaining his lead in the race for the 49th Congressional District.

With 31 percent of the precincts reporting, Issa, a Republican, had 51.5 percent, or 51,104 of the votes. His Democratic challenger, retired Marine Col. Doug Applegate, has 48,013, or 48.5 percent of the vote

Issa noted his long time in the district for why the voters are supporting him.

“I think they recognize the 16 years of service,” Issa said. “I’ve been gratified that so many people that I’ve worked with have not only endorsed me, but have gone out of their way to make public statements for me.”

UPDATE: 10 p.m., Nov. 8, 2016:

Rep. Darrell Issa has taken the lead against first-time candidate and retired Marine Col. Doug Applegate in the race for the 49th Congressional District.

With 25 percent of the precincts reporting, Issa had 51.9 percent, or 49,582 of the votes cast. Applegate had 48.1 percent, or 445,990.

With 25 percent of the precincts reporting, Applegate had 52.6 percent, or 34,000 votes. Issa had 47.4 percent, or 30,583 votes.

Issa has held the seat since 2000. In June, he was expected to easily outdistance his Democratic challenger. But the district’s changing demographics have made the district much more competitive.

Original post:

Darrell Issa has not been in a truly competitive race since he first won his congressional seat in 2000. That changed this year.

In the June primary, the incumbent was expected to easily outdistance his Democratic challenger: first-time candidate and retired Marine Col. Doug Applegate.

But Applegate surprised most observers when he kept Issa to just over 50 percent of the vote in a three-way race.

Issa is best known as a sharp partisan. During his tenure as chairman of the House Oversight and Government Reform Committee began the early investigations into Bengazi along with other hot-button targets like the Fast and Furious gun-buying program of the Bureau of Alcohol, Tobacco, Firearms and Explosives. Often considered the wealthiest man in Congress, Issa poured his own money into the recall campaign of California Gov. Gray Davis in 2003.

A combination of factors probably helped Applegate. Republicans still hold an 8 percent advantage among registered voters in the 49th Congressional District, but that margin has been closing. A late surge in registration included a number of Latino and younger voters, two groups that are not seen as favorable to Issa.

The congressman also gave his full-throated support to GOP presidential nominee Donald J. Trump. In May, Issa compared Trump to Ronald Reagan on stage at a rally in San Diego. In the weeks leading up to the general election, some polls have Trump losing to Democratic presidential nominee Hillary Clinton by more than 20 points in Southern California.

Issa has $3 million in cash on hand at the Federal Election Commission’s Sept. 30 filing deadline. Applegate raised $791,629 since becoming a candidate and had $166,821 at the deadline. That isn’t the only money in the race.

Who is supporting whom?

The district has drawn the attention of the Democratic Congressional Campaign Committee, which is running ads on Applegate’s behalf. The district is seen as one of the seats the DCCC must win if Democrats have any hope of regaining control of the House this election. In October, the nonpartisan Cook Political Report moved the 49th Congressional District to a “toss up” for the first time.

Neither side really campaigned in the primary. The tone turned negative quickly after the close finish in June. Issa released a mailer highlighting Applegate’s divorce in the early 2000s, when a judge issued two restraining orders against him. Applegate’s ex-wife issued a statement supporting him and his campaign.

An Applegate TV ad featured a 2011 New York Times article which questioned whether Issa had steered federal projects to benefit property he owned. Issa threatened Applegate with a lawsuit.

Reflecting the tightness of the race, Issa has attempted to recast himself as an independent voice. He issued a mailer featuring a large picture of President Barack Obama. The caption praises the president for signing legislation Issa supported.

The president ridiculed Issa when Obama was in the San Diego area for a closed-door fundraiser to support Applegate and other Democratic candidates.

“Now, that is the definition of chutzpah,” Obama said, according to a transcript released by The Washington Post. “Here’s a guy who called my administration perhaps the most corrupt in history - despite the fact that actually we have not had a major scandal in my administration.”

The 49th Congressional District includes Del Mar, Solana Beach, Encinitas, Carlsbad, Oceanside, Vista and San Clemente.